Bad Company is made up of two parts, each dedicated in part to how Onizuka and Ryuuji meet and get their motorcycles.

Part I
The story is told from Ryuuji's point of view, it begins when Ryuuji is trying to avoid attending class at his new school and by chance witnesses the end of a fight that Onizuka has just won. Haunted by the demonic expression on his eyes while his face is covered in blood he becomes obsessed with seeing it again, sure that one day they will have a fight from which only one of them will survive.
To his surprise, he discovers that not only he is in the same school as Onizuka but in the same class as well. Wanting to be the strongest in the school, he tries several times to bring out the demon out again, but soon realizes that Onizuka won't be angered by teenage bravados, although the rest of the bad-asses in the school are soon under his command. Ryuuji never gets the fight he desires with him (or at least at the level he desires). There is plenty of violence in Bad Company, though.
Sakura, a girl in the group of Onizuka tries to show Ryuuji the true face of her friend, and so walks him to the garage where Onizuka, Fukitoshi and Isami are mending a bike they found in a dump, this bike, by the way, is the Kawasaki Z400GP which Onizuka drives in both the sequels. Sakura tells Ryuuji that Onizuka is not the kind of person to be interested in power or who is better, he only wants to be with his friends having a good time. Ryuuji rejects it at first, again trying to pick a fight but is slowly won over and helps them in repairing the bike.
The next day, Sakura, Ryuuji and Onizuka have gone for food to celebrate just before trying the bike, but when they are back, the bike has disappeared and Fukitoshi and Isami are beaten on the floor. It turns out that the Skull Gang also had their eyes set on the bike, and so have waited for it to be repaired so they can sell it at a good price. Onizuka quickly goes to recover it, and is followed by Danma. Onizuka fights the leader of the Skulls for his bike, but the fight is interrupted by Sakura, who has brought the Wild Angels, another gang, whose leader is to become their role-model Masaki (and who is always surrounded by some kind of light-halo). After seeing the fight, Masaki asks Onizuka and the others to ride with them next time.

Part II
The boys have just found a porn magazines machine, and are trying to be bold enough to go and buy one, but to no avail, somebody always passes by. A woman approaches and buys one, with no sign of hesitation, then gets into her car and drives into them saying that no one who has seen a woman purchase a porn magazine can be left alive, but then laughs and says it was just a joke. The woman's name is Natsuki, and she drives them around town.
At the same time, Ryuuji is just entranced by her femininity, and as his parents have shut the door for him, ends up sleeping at her house. She tells him that her parents used to do the same thing, and so, they are very similar. The next day she gives him the CBX Honda she used to own. That night they go driving with the Wild Angels, everybody is very surprised, Onizuka is jealous and Ryuuji leads the way. Masaki recognizes the bike and it turns out that Natsuki used to be one of them.
The next morning Ryuuji goes again to Natsuki's house and finds she has been beaten by her boyfriend, Nezu Akira, who also bullies him. Now Ryuji has to pay him an enormous amount of money or he will be killed. After more threats, Ryuuji goes again to Natsuki's house, intending to hit him with a suspension bar.